


The Heart of the Matter

by Bludrayn23



Category: POKÉMON Detective Pikachu (2019), Pocket Monsters | Pokemon (Anime), Pocket Monsters | Pokemon - All Media Types
Genre: Anime/Movie tie-in, Character Development, Clones, Dubious Ethics, Epic Friendship, F/M, Gen, Genetic Disorders & Abnormalities, Human Experimentation, Past Character Death, Past Lives, Physical Disability, Pokemon Experimentation, Potential Relationship Development, Telepathic Bond
Language: English
Status: In-Progress
Published: 2019-06-03
Updated: 2019-06-06
Packaged: 2020-04-07 09:38:23
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 4,426
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19082389
Author URL: https://archiveofourown.org/users/Bludrayn23/pseuds/Bludrayn23
Summary: When someone takes up the mantel of Dr. Fuji's human cloning experiments, no one could possibly foresee the difficulties involved. Amber has fragmented memories of living multiple short lives in a test tube, a slew of physical impediments to overcome, and overprotective beneficiaries that don't want her to venture outside the walls of a laboratory. She just wants to define herself away from those that have created her.Meanwhile, Mewtwo still struggles to find his footing in a world mixed with humanity's travesties and wonders. But something twinges in the back of his mind - a bond he didn't know existed and certainly can't remember creating, nor the person it connects him to. Nevertheless, it may hold clues to how he relates to the rest of the world.Both embark on a journey of self discovery and meet midway to develop a friendship neither thought was possible, but forces conspire to use them against each other and threaten to tear them apart. Will they overcome the obstacles or will humanity's greed for power destroy their friendship?





	1. Matters of the Mind

**Author's Note:**

> Combines content from the anime series, the movies Mewtwo Strikes Back and Mewtwo Returns, the radio drama The Birth of Mewtwo, and the live-action Detective Pikachu movie. For those interested, the radio drama can be found with subtitles on YouTube (and is highly recommended).
> 
> I haven't written in a long time, so I'm using this little plot bunny to brush up on my skills. Updates may be sporadic and/or infrequent and may vary in length.

[ _Approximately 6 years before the events of Detective Pikachu._ ]

 

“It’s… strange. Dreaming about all the times I’ve died.”

 

Amber’s lips pinched together beneath her surgical mask as she watched the therapist jot something down frantically in her notebook from the corner of her vision. Her face was angled towards the window she sat by, in an office five stories up so that all she could see was the construction site across the street. This was her third therapist in the past five months; she’d see how quickly she could get this one to quit. There weren’t many therapists out there that had ever dealt with a situation quite like hers.

 

The therapist pushed her glasses up her nose and flipped through the patient file in her lap, then gave her patient a placid smile. “It’s normal to relive a traumatic experience in your dreams, even one that happened many years ago.”

 

Right. The traumatic experience being when her heart had stopped for five minutes when she was four years old, a whole ten years prior. Except that wasn’t what she was dreaming about, not in the least. How did one explain that she had memories of growing up multiple times in a test tube filled with fluid, only for her body to dissolve away before she reached four years of age?

 

Fortunately, the mask over her lower face prevented the therapist from seeing the bitter twist of her mouth.

 

 _‘…Ai, can you hear me?…’_ A male’s voice echoed in the dark recesses of her memory. With tremendous effort, she pushed it back as far as she could, not wanting to let slip she was having flashbacks during her waking moments as well. About a father figure that actually cared about her, unlike her guardian, who viewed her as nothing more than an artifact of science.

 

The first human clone to be born outside of a test tube.

 

Except for these pesky memories of having multiple, albeit short, lives inside of one.

 

Her hand wandered absently to the bulge below her left clavicle, where an implantable cardioverter defibrillator rested underneath her skin, keeping close track of her heart rate. Medical marvel though she was, the first successful human clone wasn’t without flaws, some of which were quite potentially deadly. And why she usually had an escort whenever she was allowed outside her carefully monitored and maintained apartment. She knew Miss Norman was right outside the door, those damnable shades over her eyes, even though they were inside a building with tinted windows, and a smartphone close at hand.

 

“What goes through your mind when you wake up after one of your nightmares?” The therapist prodded when Amber failed to comment further.

 

“Why should I tell you what I honestly think? You’ll just report it back to Dr. Clifford and give him more reason to keep me locked away.” Oops, she hadn’t meant to sound so resentful, but the truth was out nevertheless. The therapist - she refused to learn the woman’s name when she was just a lackey of Clifford Industries - opened her mouth to refute the accusation, but Amber was quick to cut it off. “Don’t bother, I know I have no privacy when it comes to my health, physical or otherwise.”

 

The silence was heavy between them as Amber continued to stare out the window. She wondered what it would be like to walk the streets below on a regular basis. To be able to stop at the shopping mall with friends after school, or see a movie in an actual theater. It would be a serendipitous feeling to act like a normal fourteen year old, instead of a disabled science experiment.

 

“How is your studying going?” The therapist tried to steer her toward a less offensive topic instead.

 

“I’ll complete my senior courses by next spring,” she answered blandly.

 

“Well, that’s certainly impressive! Aren’t you proud of graduating so much earlier than your contemporaries?”

 

“What contemporaries?” Amber bristled. “I don’t get to attend classes, so I don’t have classmates, therefore no contemporaries. What’s to be proud of when all my time is spent inside, studying? God forbid I take a step outside and I break something the doctors have to fix!” She finally shifted her gaze to meet the woman’s eyes, her chilly cobalt blue against sympathetic brown behind optical frames. “Can you even begin to fathom how lonely my existence is? Sometimes I really, really wish Dr. Clifford hadn’t made me.”

 

“You consider yourself to be made? Not born?”

 

_‘…I don’t even care if I’m not the real thing… I'm sure living is wonderful…’_

 

Amber felt a jolt in her chest - not electrical, but emotional, from the truth behind the words, clashing with the young voice of a girl in her head. Without another word, she braced her hands on the armrests of her chair and began to shove herself up, a pained hiss slipping out from between clenched teeth. She’d revealed way too much, way too early in the session to this woman. While her body was fragile to a fault, her feelings were supposed to be an impenetrable fortress. She couldn’t afford an existential crisis right now.

 

The therapist rose up and stepped forward as if to stop her, but after a moment of thought, she stopped with a slight inclination of her head. “Very well,” she concluded, “I think that’s enough progress for today.”

 

She wanted to snap back, “What progress?” But the monitor on her wrist started to whine as her heart rate spiked and before she could even take a step on her own, Miss Norman came through the door, pushing a wheelchair in front of her. Well, so much for “storming out” of the session on her own power, she mused as the weak muscles in her limbs struggled to support her.

 

There was nothing more humiliating that having to be wheeled out of counseling session by her guardian’s assistant-slash-Pokemon partner. She wasn’t even allowed to wheel herself because Miss Norman would slap her hands (gently) back into her lap. Fortunately, the ride down the elevator was short, but long enough for her to steel herself for what was going to be a very uncomfortable ride back to the small apartment room in the Clifford Industries building.

 

However, instead of an ominous black SUV, there was a sporty, obnoxiously red convertible parked at the curb. A handsome man with coiffed blonde hair and a pair of sunglasses leapt out from the driver’s side and shooed Miss Norman to the side, a beam on his face.

 

“Well, you lasted longer in there than I thought you would, little dove,” Roger Clifford said in his excessively posh accent, rolling her to the passenger side and opening the door, but letting her do the rest. He knew better than to baby her and simply offered an arm for her to grasp as she heaved herself out of the chair and slid into the seat. Without missing a beat, he collapsed the wheelchair and set it in the trunk.

 

“Where the hell have you been hiding for the past month?” asked Amber, her lips curling upward into the first smile she’d had in a while as she leaned into the leather passenger seat, warm from the sun. Although she despised the elder Clifford, especially after he deemed her as a failure to his crusade to improve the human condition, she admittedly adored the son. He’d been as close as a brother to her during the years that Dr. Clifford disappeared and left her in the hands of C.I.-paid researchers.

 

The corner of Roger’s mouth quirked up, noting that Amber didn’t sound mad, just amused, and waved jauntily at Miss Norman, revving the engine tauntingly before pulling away from the curb. “Well, dear old dad and his degenerative disease decided to step back a bit from running the family business, so I’ve been picking up the slack,” he explained, a hint of derision in his voice. “But I felt a little reunion was overdue, so I came to steal you away from your mute bodyguard.”

 

Amber rolled her eyes, enjoying the feel of the wind in her hair. Feeling reckless, she pulled the face mask down and drew in a deep breath, the smell of car exhaust and warm asphalt assaulting her nose. For a brief moment, as they drove down Main Street, she pretended she was a normal person in Ryme City, and grinned at the passerby’s and their Pokemon going about their days. For just a couple of seconds, she wasn’t a defective human clone with disjointed memories of different lives, but a normal girl with a big brother who loved her.

 

For the time being, that would have to be enough.

 

* * *

 

[ _Twelve years prior._ ]

 

The night was cool, without a cloud in sight, and Mewtwo tugged his cloak closer to his body as he crouched on the ledge of a skyscraper. He watched the streets below as the last trickle of humanity wrapped up their late night activities. This was his favorite part of the day, where he didn’t have to be quite as cautious about what he did and who saw him, because most of the town’s denizens were already asleep. There were always a few stragglers, but changing the memories of a few humans was inconsequential compared to ousting himself to all of mankind, especially when they weren’t ready to come to terms with his existence.

 

Quite frankly, he still had trouble coming to terms himself. It had been a couple months since he had left Purity Rock to explore the human world and perhaps discover where he fit in the grand scheme of things. Half of the Pokemon copies from the lab had ventured out as well, while the rest remained at Purity Rock, and for once he didn’t feel like he was responsible for every one of them, even though he created them. After all, it was the right of every sentient being to carve out their own path in the world.

 

The air buzzed as he gathered his power around him and levitated down to the empty street. It was fascinating to see how humans lived up close. Granted, some of it was rather gross. They didn’t always pick up after themselves, he mused, flicking his hand to summon a wrinkled mess of paper from the ground. It was a newspaper - a primitive means of transferring a large amount of data to the general populace, that changed daily with new information.

 

He smoothed out the cover, curious despite himself. He’d learned to read back on New Island during his scheme to prove copies like himself were superior to the originals. A scheme that definitely hadn’t gone as planned, but he couldn’t say that he regretted any of it because it ultimately led him to his current path of self discovery.

 

The sky was clear, so the light reflecting from the moon was enough to make out the print. Even before he read the headline, a feeling of trepidation started to coil in the lower pits of his abdomen. Partially because he recognized the picture of the man featured on its front page - a face he couldn’t quite comprehend seeing because it belonged to a dead man. The one who created him...

 

 

 

 

> _‘Deceased Doctor’s Dream Finally Achieves Actualization’_
> 
>  
> 
> _Two years ago a mysterious explosion destroyed a laboratory on New Island, taking the scientists and their research with it. Everything was believed to be lost, until owner of Clifford Industries, Dr. Howard Clifford came forward with a breakthrough in human genetics._
> 
>  
> 
> _“Dr. Fuji, the geneticist responsible for the majority of the discoveries made on New Island, was both an intelligent and distrustful man, for good reasons. The benefactor for the New Island laboratory has never been uncovered even to this day, so it isn’t that much of a surprise that Dr. Fuji took certain measures to back up his research off-site from the facility,” Dr. Clifford explained._
> 
>  
> 
> _When Dr. Clifford received a strange disk in the mail, he hadn’t expected years of Dr. Fuji’s research into human genetics and the potential of cloning to fall into his lap. Although colleagues that went to the same university together, Dr. Clifford hadn’t been particularly close to the late geneticist. “I knew he lost a daughter in a tragic car accident, which galvanized a fierce dedication to the subject of cloning. When the data pulled up on my computer and I saw how far he got, I felt it necessary to continue his research in both their honors.”_
> 
>  
> 
> _Dr. Clifford himself has a keen interest in genetics and improving the overall human condition. Diagnosed with a degenerative spine disease that will in the near future restrict his mobility and confine him to a wheelchair, Dr. Clifford believes that the first step to altering the human DNA is perfecting its replication. While Dr. Fuji’s experiments could not successfully support a human clone past four years, Dr. Clifford created a method that improved the survivability of the subject._
> 
>  
> 
> _“Much of the physical development took place in a test tube, so while the cloned subject was technically alive, it had never been born. I wanted to take a more natural approach and see if undergoing the birthing process would have an impact on the subject’s development. We have yet to see if they will survive past the maximum four years Dr. Fuji was able to reach,” interview continued on page 5…_

 

A gust of wind tore the paper out of Mewtwo’s hand and halfway into the gutter, but he was too lost in thought to care. The entire laboratory had been razed to the ground in his uncontrolled anger. Nothing could have survived, but that didn’t mean that information previous to the destruction hadn’t somehow been transferred elsewhere. But why weren’t the experiments on Pokemon cloning mentioned?

 

A pulse of pain hit him between the eyes as he searched his scant memories of the original lab, before he rebuilt it. Large glass test tubes filled with ochre-colored liquid. The sound of researchers constantly bustling about the room. Drifting on the precipice of consciousness…

 

_‘…Don’t cry. You’re going to live. Live, ok? I'm sure that living is wonderful…’_

 

It felt like a needle sliding into his eye, the more he tried accessing those faint, ever so distant echoes, hardly substantial enough to even be considered memories. With a huff of breath, he released his focus on the futile task and the pain immediately eased. Why were there wisps of memories that obviously existed but couldn’t be accessed? What had happened that his mind closed them up? To prevent him from reliving something painful? He’d never been afraid of pain. It was mere physical stimulus that simply confirmed that he was indeed alive.

 

It seemed like his time of aimless wandering was over, at least. He needed to investigate this Dr. Howard Clifford, make sure he wasn’t meddling with Pokemon genetics. There was no reason to let another unfortunate creation like himself be born, destined to feel a disconnect from the rest of the world. And if the doctor was only experimenting with humans, well, Mewtwo didn’t feel quite as beholden to stop him.

 

He reached out with his powers, seeking the newspaper and bringing it back to his hands. The remainder of the article didn’t give any clues to where Dr. Clifford lived, so he would have to get creative. Smoothing the wrinkled pages out, he searched the front for the best lead - the name of who wrote the article. While the newspaper was almost five days old, it was local, not regional. If he tracked down the publisher, finding the author would be the next logical step. After all, journalists were notorious for only revealing the parts that made good news. It was what had been omitted that could lead him to Dr. Clifford.

 

A large shuffle came from an alleyway to the left and without a blink, Mewtwo shot back up into the sky. While it was most likely a wild Pokemon rummaging about, he didn’t want to risk being seen by a human. He still wasn’t convinced that the human world was ready to learn of his existence, except the three trainers who had aided him at Purity Rock.

 

Maybe one day.

 

But not today.


	2. Intermission: Timeline Data

**Notes for the Chapter:**

> I have gone back over chapter one to correct some timeline mistakes and decided it would be prudent to share my notes. I apologize for this not being an actual chapter, the next which I plan to complete over the weekend, but the story tends to jump around time wise, so I wanted to make sure everyone is on the same page as I am.
> 
> I do want to thank those that have left kudos and comments. I'm still not sure where all of this will go, but I'm glad you've at least enjoyed the beginning.

Will contain content spoilers for the following: radio drama The Birth of Mewtwo, anime short The Uncut Story of Mewtwo’s Origin, anime movies Mewtwo Strikes Back and Mewtwo Returns, and live-action movie Detective Pikachu. Will only contain fanfic spoilers from chapter one.

 

For the sake of clarity and because of inconsistencies between mediums, I will be taking some creative liberty in the anime to live-action movie timeline, as well as making some assumptions to make the storyline more cohesive. Before I touch on the timeline, I would like to address the inconsistencies and the assumptions I will make based on them, as well as explain some of the differences between The Birth of Mewtwo radio drama (transcripts of which can be read [here](http://www.rigelatin.net/copycat/saga/origin/drama.php)) and The Uncut Story of Mewtwo’s Origin from the Japanese version of the first Pokemon movie.

 

Firstly, the main differences meaningful to the story between the radio drama and the anime adaptation of Mewtwo’s creation. In the anime, Dr. Fuji only replicates Ai’s neural pattern, not her body. In the radio drama, he recreates her whole body (assumed from the context of the drama and the art included with the CD’s booklet found [here](http://www.rigelatin.net/copycat/media/drama/index.php)). Also, in the anime adaptation, the Pokemon clones disappear with Aitwo. However, in the drama, cloning Pokemon from the original source has already been perfected. Humans, however, not so much. Later, in the adaptation, Mewtwo is attacked by the laboratory’s security system and he reflects it, while in the radio drama, the security system kills him and he regenerates. I will be deferring to the radio drama version for the purposes of this story.

 

Secondly, some inconsistencies and the assumptions I’m making to help with the consistency of the story. In both the radio drama and anime adaptation, human copies have never survived past four years. While it’s not specified how long Aitwo has been alive in the test tube, she must be close to her four year limit when Mewtwo is created. In addition, she probably isn’t even Aitwo, but ‘three or ‘four, because Dr. Fuji must have created previous copies to know that a human clone cannot survive past the declared four years (however, I will continue to refer to her as Aitwo for simplicity’s sake). Furthermore, Aitwo’s language skills far surpass that of a 4 year old’s, so I am going to assume that for both Aitwo and Mewtwo, Dr. Fuji found a way to accelerate their growth within the tanks, which would most likely suit Giovanni’s purposes. Therefore, I am going to take the liberty and say that after Aitwo dies and Mewtwo is forcibly sedated, they accelerate his growth and he reaches a mature body within a year.

 

Finally, to avoid confusion, the original Ai and Dr. Fuji’s clones will be referred to by their Japanese names, while the newest clone created by Dr. Clifford will be referred to by the English name, Amber.

 

Onto the timeline, which will cover events from the radio drama, anime, movies, and chapter one of the fanfic.

 

According to Dr. Laurent in Detective Pikachu, Mewtwo fled the Kanto region around 20 years ago, so we start at a very minimum of 20 years prior to the live-action movie.

 

Sometime before the fossilized eyelash of Mew is discovered, Ai Fuji dies in a car crash and her father, unable to accept that she is gone, decides to try and clone her. Though not relevant to this story, his inability to let go causes Ai’s mother to leave him, which only strengthens his resolve to clone her.

 

A Team Rocket expedition discovers the fossil and Giovanni (presumably already aware of Dr. Fuji’s exploits in cloning) recruits Dr. Fuji to make a clone of it. Dr. Fuji agrees, if only to discover how to prolong the lifespan of human clones. The fossil is taken to his lab on New Island and within a month he is able to create Mewtwo. Note: Aitwo is already in existence and has been for at least three years, but less than four.

 

Over a short amount of time, Aitwo and Mewtwo become acquainted, somehow able to communicate telepathically between their test tubes. However, Aitwo is near the end of her four year lifespan and she dies, which Mewtwo witnesses. He becomes distressed over losing his friend and Dr. Fuji’s callousness about being able to create more Ais. The scientists are forced to administer a sedative and keep him unconscious while continuing the experiment.

 

Mewtwo’s powers increase while he grows rapidly until, triggered by internal existential distress, he shatters his test tube. Confused, he lashes out and the laboratory’s security system kills him. However, he regenerates and the scientists, including Dr. Fuji, are thrilled to have created the strongest Pokemon. Dissatisfied with their explanations of creating him and unsure of his purpose, he destroys the lab and everyone in it.

 

Immediately afterwards, Giovanni arrives on the island and convinces Mewtwo that he can prove his strength by cooperating with Team Rocket. He accepts restricting chains and armor that dampen his powers, so they don’t destroy everything.

 

Over the next couple of months, Mewtwo defeats the Pokemon and trainers Giovanni puts in front of him, allowing Team Rocket to catch an exorbitant amount of Pokemon. He develops a strong distaste for humans while in their company. When Giovanni asserts that Mewtwo’s worth is measured only by how useful he is to humans, Mewtwo rebels and breaks through the armor and chains to destroy Team Rocket’s headquarters.

 

Around this time, Dr. Howard Clifford receives an unmarked disk in his mail. When he loads it, he discovers Dr. Fuji’s work, which appears to be relevant to his desire to improve the human condition. It is still unknown who sent him the data.

 

Mewtwo returns to New Island and rebuilds the laboratory underneath a castle in a very short amount of time. (According to the anime, Team Rocket headquarters is destroyed in episode 65 and the events of the movie happen before episode 66.) He tracks down some of the strongest trainers in the Kanto region and invites them to New Island to prove that Pokemon copies are superior to the originals. The main events of Mewtwo Strikes Back takes place.

 

Afterwards, Mewtwo erases the memories of those on New Island and leaves the Kanto region with the Pokemon copies to try and find a safe home for them. [This takes place about 20 years prior to the Detective Pikachu movie.]

 

Mewtwo and the copies settle on Mount Quena in the Johto region. The storms prevent casual passerby’s from discovering their location. For the next two years, Mewtwo and the copies live in peace, unaware that Giovanni has been trying to track Mewtwo using the Team Rocket satellites.

 

In the meantime, Dr. Clifford has run numerous experiments with Dr. Fuji’s data. A human clone, named Amber, is successfully born.

 

A Team Rocket satellite captures a grainy image of Mewtwo and Giovanni sets out to reacquire him. Mewtwo surrenders himself after Giovanni threatens to experiment on the Pokemon copies and is subjected to torture when he refuses to obey his orders. Pokemon trainer Ash and friends rescue him and Mewtwo rejuvenates in the healing spring waters of Mount Quena, after which his powers seem to increase further and his mind isn’t quite as clouded from existential doubt. He relocates the spring underneath the mountain and erases the memories of Team Rocket and those that could threaten the existence of the healing springs, but allows Ash and his companions to remember. Some of the Pokemon copies decide to stay under Mount Quena, while others depart to find their own places in the world. Mewtwo also decides to leave Mount Quena and ventures out into the world.

 

Within a couple months of leaving Mount Quena, Mewtwo discovers that the research from the original laboratory was not completely destroyed and that someone is continuing Dr. Fuji’s work. He decides to investigate further. [It is now 18 years prior to the Detective Pikachu movie and Amber is 2 years of age.]

 

Elsewhere, two years later, human clone Amber turns four and, reminiscent of the four year limit of Dr. Fuji’s clones, experiences a severe cardiac event. Her heart stops for five minutes before the doctors are able to resuscitate her. It’s decided she requires an ICD and while she ultimately survives, Dr. Clifford deems human cloning an overall failure and searches for other ways to improve humanity, leaving Amber in the custody of his son Roger Clifford and a team of doctors that have been with her since her birth. [It is now 16 years prior to the Detective Pikachu movie.]

 

Dr. Clifford is gone for several years traveling the world and comes back with the conclusion that humanity can only improve alongside the Pokemon, so he decides to build a city where humans and Pokemon can coexist without Pokeballs and battles. Between travel and construction, approximately 6 years pass before Ryme City has its first annual Pokemon parade. [It is now 10 years prior to the Detective Pikachu movie.]

 

Four more years pass, finding Amber at 14 years of age and 6 years prior to the Detective Pikachu movie. She is in therapy for nightmares attributed to her near death experience and becoming increasingly frustrated with the restrictions placed on her by her doctors and Dr. Clifford because of her frail condition.

 

A couple of months before the events of the Detective Pikachu movie, PCL builds a new containment chamber and Dr. Clifford hires Detective Harry Goodman to track down and capture Mewtwo. It is unclear how Detective Goodman captures him. PCL’s experiments on Mewtwo produce a compound called ‘R’ that reduces Pokemon to a feral state. The compound is tested at illegal Pokemon battles, which gains the attention of the Ryme City Police Department. Dt. Goodman is assigned to the case and he eventually tracks it back to Dr. Clifford, PCL, and Mewtwo. Undergoing a change of heart, Dt. Goodman and his partner Pikachu decide to free Mewtwo. They are successful, but are believed to perish in a car crash shortly after leaving PCL. Tim Goodman is alerted and the rest of the events of the Detective Pikachu movie take place.

**Notes for the Chapter:**

> I hope this helps clear up any confusion. The fanfic will now catch up with Mewtwo's search for more information on the new cloning experiments and a shocking discovery within his own mind.


End file.
